Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1807 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0431599562 sf0431414457 4 31599562 1.46E-09 NA
vg1217311558 sf1217305513 12 17311558 4.28E-09 NA
vg0525487385 sf0525424806 5 25487385 5.47E-09 NA
vg1021046076 sf1020974555 10 21046076 8.62E-09 NA
vg1124292282 sf1123826152 11 24292282 1.01E-08 NA
vg0139694264 sf0139693221 1 39694264 2.27E-07 NA
vg0412432479 sf0412423193 4 12432479 8.35E-06 1.15E-06